I just encountered an interesting issue where running something as root disallows me to change the fonts of root applications.
Now, this is a weird one so stick with me, but I encountered my issue in Cosmic while using gdebi-gtk. What would happen is everything appears as I had specified… until gdebi-gtk reloads as root to install a program. The installation dialog shows up and has none of my settings were applied. The application itself does, but not the dialogs thereafter.
I had to enable manual login use the root account to fix this. There has got to be a better way.